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Table 1 Phylogenetic classification, nucleotide sequence variations and frequency of HPV-16 E6 variants identified in women from Southern Mexico

From: Association of human papillomavirus 16 E6 variants with cervical carcinoma and precursor lesions in women from Southern Mexico

Variants

HPV 16 E6 nucleotide position

Predicted amino acid change E6 protein (151 aa form)

Frequency

 

109

110

131

132

143

145

176

182

183

185

188

189

256

257

271

286

289

306

310

335

350

403

424

442

532

535

 

N=330

%

HPV 16R

T

C

A

G

C

G

G

A

T

T

G

A

C

A

T

T

A

A

C

C

T

A

A

A

A

A

   

Lineage EAS/Sublineage EUR

Class E-T350

                           

51

15.45%

E-Prototype

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

No change

43

13.03%

E-G131

-

-

G

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

R10G

8

2.42%

Class E-G350

                           

220

66.67%

E-G350

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

L83V

132

40.00%

E-C109/G350

c

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

L83V

6

1.82%

E-G110/G350

-

G

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

Q3E/L83V

2

0.61%

E-G131/G350

-

-

G

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

R10G/L83V

2

0.61%

E-G131/C188/G350

-

-

G

-

-

-

-

-

-

-

C

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

R10G/E29Q/L83V

2

0.61%

E-A176/G350

-

-

-

-

-

-

A

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

D25N/L83V

17

5.15%

**E-A176/G424/G350

-

-

-

-

-

-

A

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

g

-

-

-

D25N/L83V

1

0.30%

E-T182/G350

-

-

-

-

-

-

-

T

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

I27L/L83V

4

1.21%

E-C182/G350

-

-

-

-

-

-

-

C

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

I27L/L83V

2

0.61%

**E-C183/G350

-

-

-

-

-

-

-

-

C

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

I27T/L83V

3

0.91%

E-G185/G350

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

L28V/L83V

2

0.61%

E-A188/G350

-

-

-

-

-

-

-

-

-

-

A

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

E29K/L83V

1

0.30%

E-C188/G350

-

-

-

-

-

-

-

-

-

-

C

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

E29Q/L83V

39

11.82%

**E-C188/G310/G350

-

-

-

-

-

-

-

-

-

-

C

-

-

-

-

-

-

-

G

-

G

-

-

-

-

-

E29Q/F69L/L83V

2

0.61%

**E-G189/T256/G350

-

-

-

-

-

-

-

-

-

-

-

G

t

-

-

-

-

-

-

-

G

-

-

-

-

-

E29G/L83V

1

0.30%

E-G257/G350

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

-

-

G

-

-

-

-

-

I52L/L83V

1

0.30%

**E-C306/G350

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

C

-

-

G

-

-

-

-

-

K68T/L83V

1

0.30%

E-C442/G350

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

C

-

-

L83V/E113D

1

0.30%

**G535/G350

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

G

-

-

-

-

g

L83V

1

0.30%

Lineage AA/NA/Sublineage AA1

Class AA-a

                           

36

10.91%

AA-a

-

-

-

-

-

T

-

-

-

-

-

-

-

-

-

a

g

-

-

T

G

-

-

-

g

-

Q14H/H78Y/L83V

35

10.61%

**AA-a/C188

-

-

-

-

-

T

-

-

-

-

C

-

-

-

-

a

g

-

-

T

G

-

-

-

g

-

Q14H/E29Q/H78Y/L83V

1

0.30%

Class AA-c

                           

22

6.67%

AA-c

-

-

-

-

-

T

-

-

G

-

-

-

-

-

-

a

g

-

-

T

G

-

-

-

g

-

Q14H/I27R/H78Y/L83V

20

6.07%

**AA-c/G185

-

-

-

-

-

T

-

-

G

G

-

-

-

-

-

a

a

-

-

T

G

-

-

-

g

-

Q14H/I27R/L28V/H78Y/L83V

1

0.30%

AA-c/C271

-

-

-

-

-

T

-

-

G

-

-

-

-

-

c

a

g

-

-

T

G

-

-

-

g

-

Q14H/I27R/H78Y/L83V

1

0.30%

Lineage AFR2/Sublineage Afr2a

Class Af2-a

                           

1

0.30%

Af2-a/C109/G403

c

-

-

T

G

T

-

-

-

-

-

-

-

-

-

a

g

-

-

T

-

g

-

-

-

-

R10I/Q14D/H78Y

1

0.30%

  1. HPV 16 R: reference sequence. Predicted amino acid change: the amino acid numeration was done using the 151 amino acid E6 oncoprotein form as reference. Capital letters indicate polymorphisms that produce amino acid change. Lower-case letters indicate silent mutations. – Indicate no polymorphism. Italic letters indicate new polymorphisms. Italic capital letters indicate amino acid change. **Indicate new variants.
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